gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] sql change table

[<fed...@bi...>]

Thanks Poliana,
I tried as you suggest; no error appeared but I had always the same reply:
'0 rows updated'.
I connect to Oracle as 'sys/password as sysdba'.
Any other ideas about how to solve the problem?
Thanks
Federica


> Hi Federica,
>
> Try
>
> UPDATE core.userinfo SET login='your_login', password='your_password'
> WHERE user_id = 1;
>
> Poliana
>
>
> On Wed, 9 Feb 2005 18:32:14 +0100 (CET), fed...@bi...
> <fed...@bi...> wrote:
>> Hi guys, I'm Federica! Some months ago I had some problems with GUS
>> installation; then I had to perform other tasks, and after that I
>> decided
>> to delete everything and restart all!!
>> I have got a new problem. I've never used sql before: I can't change the
>> login, password and group in the core.userinfo, core.groupinfo,
>> core.projectinfo tables! For example when I try to select or update some
>> rows of core.userinfo table the replay is always: 0 rows
>> selected/updated.
>> Anyone can help me?
>> Thanks, Federica
>>
>> -------------------------------------------------------
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>
>
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Re: [Gusdev-gusdev] Two Bugs _with_ LoadSequenceOntology

[Joan M. <ma...@pc...>]

Yes, if I remember correctly, I asked Mike to change these, so_id and 
definition to varchar2(32), varchar2(4000) so I could load the table.

Ed Robinson wrote:

>There are two bugs _with_ (not in) LoadSequenceOntology, one
>of which needs to be fixed in the 3.5 release.
>
>The main one is the the sres-tables.sql DDL in
>$project_home/Model/schema/oracle declares so_id as a number,
>it needs to be varchar2.  All so_ids begin with SO.  I won't
>touch these scripts in CVS.
>
>also, since we are loading the SO annotations which have very
>big descriptions, we either need to increase the definition
>field size from 255 characters or truncate the field in the
>plugin.  Where do we want to make the change?
>
>-Ed
>
>-----------------
>Ed Robinson
>Center for Tropical and Emerging Global Diseases
>University of Georgia, Athens, GA 30602
>ero...@ug.../(706)542.1447/254.8883
>
>
>-------------------------------------------------------
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>  
>

-- 
Joan Mazzarelli, Ph.D.
Computational Biology and Informatics Laboratory
Center for Bioinformatics
University of Pennsylvania
1429 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104
ma...@pc...
Ph:215-573-4413 FAX:215-573-3111

[Gusdev-gusdev] Two Bugs _with_ LoadSequenceOntology

[Ed R. <ero...@ug...>]

There are two bugs _with_ (not in) LoadSequenceOntology, one
of which needs to be fixed in the 3.5 release.

The main one is the the sres-tables.sql DDL in
$project_home/Model/schema/oracle declares so_id as a number,
it needs to be varchar2.  All so_ids begin with SO.  I won't
touch these scripts in CVS.

also, since we are loading the SO annotations which have very
big descriptions, we either need to increase the definition
field size from 255 characters or truncate the field in the
plugin.  Where do we want to make the change?

-Ed

-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

Re: [Gusdev-gusdev] LoadSequenceOntology

[mazz <ma...@pc...>]

I created a tab delimited file which I used for this plugin from a file at 
the source forge site.

I have attached the file which the plugin uses.

Joan










On Wed, 9 Feb 2005, Ed Robinson wrote:

> Has anyone used the LoadSequenceOntology plugin before?  The
> plugin takes a tab delimited file as its input, but SO does
> not provide a tag delimited file.  This plugin probably needs
> to be re-written to work with the source DAGs, but I would
> prefer a quick and dirty solution in the meantime.
>
> Any suggestions would be appreciated.
>
> -Ed
> -----------------
> Ed Robinson
> Center for Tropical and Emerging Global Diseases
> University of Georgia, Athens, GA 30602
> ero...@ug.../(706)542.1447/254.8883
>
>
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[Gusdev-gusdev] proposal for nested records in WDK

[Steve F. <sfi...@pc...>]

folks-

here is what dave and i worked up.

comments encouraged.

MODEL
In the Model XML file:
  - in <recordClass>
         - lose <tableQuery>
         - add <nestedRecord>
         - add <nestedRecordList>

<nestedRecord> and <nestedRecordList> are identical except that the 
former has cardinality 0 or 1 and the latter 0, 1 or more.

They each specify:
   - a reference to a query that provides primary keys for the nested 
records.  the query can have interpolated into it any attribute values 
from the containing record
  - a reference to a recordClass.  This specifies the type of the nested 
record

A given recordClass can have 0, 1 or more <nestedRecord>s and/or 
<nestedRecordList>s

Circular references are allowed.   (Eg, a Gene can have an RNA and vice 
versa)


VIEW
A summary display still shows only attributes of a record, not nested 
records.  

A detail display shows shows its nested records in summary form.   
Display of a nestedRecordList will look a lot like the current table 
display.  A nestedRecord will be similar, but have only one row.

In addition to the current ability to customize a detailed view for a 
record class (by providing a .jsp page named for the record class) we 
will introduce:
   - a customizable view for a nestedRecord.  the .jsp file will be 
named xxxxxxxxxSummary.jsp where xxxxxxxxxx is the name of the record 
class.   (this won't be used for a standard summary page, just for a 
nested record summary)
  - a customizable view for a nestedRecordList.    the .jsp file will be 
named xxxxxxxListSummary.jsp

The .jsp files for nested records and lists will be dropped into the 
detail page of the containing record.   We anticipate using this as the 
hook for plugging in graphics to a detail page

steve

[Gusdev-gusdev] LoadSequenceOntology

[Ed R. <ero...@ug...>]

Has anyone used the LoadSequenceOntology plugin before?  The
plugin takes a tab delimited file as its input, but SO does
not provide a tag delimited file.  This plugin probably needs
to be re-written to work with the source DAGs, but I would
prefer a quick and dirty solution in the meantime.  

Any suggestions would be appreciated.

-Ed
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

Re: [Gusdev-gusdev] Java errors on building GUS install -append

[Dave B. <db...@pc...>]

As a temporary fix to this problem, add the -skipJavaCompiling flag to=20
your build command:

build GUS install -append -skipJavaCompiling.

However, this is sometimes indicative of trouble connecting to your=20
database instance of GUS to retrieve the schema necessary for building the=
=20
Perl and Java object layers (if that makes no sense, don't worry about it=
=20
for now until you have successfully installed GUS and have begun to=20
familiarize yourself with it).

Dave

On Wed, 9 Feb 2005 fab...@de... wrote:

> Hi all,
>
> I'm trying to install GUS with PostgreSQL in my machine. I've already fol=
lowed
> the steps in the documentation
> (http://www.gusdb.org/documentation/install-setup.html)  with the Postgre=
s
> Schema. All Ok!!! But when I have to execute the command "build GUS insta=
ll
> -append". I got many, many, many, many java errors.
>
> All the errors are:
>
> [javac]
> /usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes/Enzym=
eClassAttribute_Table.java:17:
> error: Missing term.
>    [javac]         tableAtts.put("attribute_value", new
> GUSTableAttribute("attribute_value", "text", "java.lang.notdefyet", -1, ,=
 -1,
> false, false) );
>
> In different classes!!
>
> Does anyone know something about it???
>
> P.S.: Is it possible build GUS installation without edit the file
> $GUS_HOME/config/schema.prop to PostgreSQL database??? I noticed this fil=
e has
> many references to ORACLE not to PostgreSQL. No problem???
>
> Thanks a lot!
>
> Fabr=EDcio
>
> -------------------------------------------------
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>
>
> -------------------------------------------------------
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> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
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>

Re: [Gusdev-gusdev] Java errors on building GUS install -append

[Michael S. <msa...@pc...>]

Hello,

The Java Object layer doesn't currently support PostgreSQL.  This will=20
be fixed in the upcoming GUS 3.5 release (due within weeks).

Also, I don't believe the current PostgreSQL system requires=20
schema.prop, but this has also changed for GUS 3.5

--Mike


fab...@de... wrote:
> Hi all,=20
>=20
> I'm trying to install GUS with PostgreSQL in my machine. I've already f=
ollowed
> the steps in the documentation
> (http://www.gusdb.org/documentation/install-setup.html)  with the Postg=
res
> Schema. All Ok!!! But when I have to execute the command "build GUS ins=
tall
> -append". I got many, many, many, many java errors.=20
>=20
> All the errors are:
>=20
> [javac]
> /usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes/Enz=
ymeClassAttribute_Table.java:17:
> error: Missing term.
>     [javac]         tableAtts.put("attribute_value", new
> GUSTableAttribute("attribute_value", "text", "java.lang.notdefyet", -1,=
 , -1,
> false, false) );
>=20
> In different classes!!
>=20
> Does anyone know something about it???
>=20
> P.S.: Is it possible build GUS installation without edit the file
> $GUS_HOME/config/schema.prop to PostgreSQL database??? I noticed this f=
ile has
> many references to ORACLE not to PostgreSQL. No problem???
>=20
> Thanks a lot!
>=20
> Fabr=EDcio
>=20
> -------------------------------------------------
> This mail sent through IMP: http://horde.org/imp/
>=20
>=20
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_ide95&alloc_id=14396&op=CCk
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] Java errors on building GUS install -append

[<fab...@de...>]

Hi all,=20

I'm trying to install GUS with PostgreSQL in my machine. I've already fol=
lowed
the steps in the documentation
(http://www.gusdb.org/documentation/install-setup.html)  with the Postgre=
s
Schema. All Ok!!! But when I have to execute the command "build GUS insta=
ll
-append". I got many, many, many, many java errors.=20

All the errors are:

[javac]
/usr/local/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes/Enzym=
eClassAttribute_Table.java:17:
error: Missing term.
    [javac]         tableAtts.put("attribute_value", new
GUSTableAttribute("attribute_value", "text", "java.lang.notdefyet", -1, ,=
 -1,
false, false) );

In different classes!!

Does anyone know something about it???

P.S.: Is it possible build GUS installation without edit the file
$GUS_HOME/config/schema.prop to PostgreSQL database??? I noticed this fil=
e has
many references to ORACLE not to PostgreSQL. No problem???

Thanks a lot!

Fabr=EDcio

-------------------------------------------------
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Re: [Gusdev-gusdev] sql change table

[Poliana M. <pol...@gm...>]

Hi Federica,

Try

UPDATE core.userinfo SET login='your_login', password='your_password'
WHERE user_id = 1;

Poliana


On Wed, 9 Feb 2005 18:32:14 +0100 (CET), fed...@bi...
<fed...@bi...> wrote:
> Hi guys, I'm Federica! Some months ago I had some problems with GUS
> installation; then I had to perform other tasks, and after that I decided
> to delete everything and restart all!!
> I have got a new problem. I've never used sql before: I can't change the
> login, password and group in the core.userinfo, core.groupinfo,
> core.projectinfo tables! For example when I try to select or update some
> rows of core.userinfo table the replay is always: 0 rows selected/updated.
> Anyone can help me?
> Thanks, Federica
> 
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] sql change table

[<fed...@bi...>]

Hi guys, I'm Federica! Some months ago I had some problems with GUS
installation; then I had to perform other tasks, and after that I decided
to delete everything and restart all!!
I have got a new problem. I've never used sql before: I can't change the
login, password and group in the core.userinfo, core.groupinfo,
core.projectinfo tables! For example when I try to select or update some
rows of core.userinfo table the replay is always: 0 rows selected/updated.
Anyone can help me?
Thanks, Federica

Re: [Gusdev-gusdev] Core.AlgorithmParam: Another column size problem

[Steve F. <sfi...@pc...>]

ok.

there is probably a limit to how big a string can be passed through the 
unix shell command processor.

often the sql passed in is not arbitrary but conforms to an sql 
template.   in that case, the template can be hard coded into the plugin 
and parameters for it passed into the plugin.

or, the sql can be put in a file

steve

Josef Jurek wrote:

>While recently working with one of our locally written plugins
>which takes a SQL statement as an argument, this plugin failed
>because of of the size of the field STRING_VALUE in the
>Core.AlgorithmParam table:
>
>   SQL> describe Core.AlgorithmParam;
>    Name                                      Null?    Type
>    ----------------------------------------- -------- ----------------------------
>    ALGORITHM_PARAM_ID                        NOT NULL NUMBER(10)
>    ALGORITHM_PARAM_KEY_ID                    NOT NULL NUMBER(5)
>    STRING_VALUE                                       VARCHAR2(1000)
>   [...]
>
>The SQL statement I tried to run through the plugin exceeded
>1000 characters.  I would think that SQL arguments would be
>common for GUS plugins, and we use such plugins often at the
>Preuss Lab.  A solution to this immediate problem would be to
>increase the STRING_VALUE column to VARCHAR2(2000), though
>eventually I or someone else may exceed this limit as well.
>
>Just letting people know problems we are running into.
>
>Thanks, Josef
>
>
>Josef Jurek, Ph.D.
>
>Daphne Preuss Laboratory
>Molecular Genetics and Cell Biology
>The University of Chicago
>ju...@cs...
>
>voice: (773) 834-3985
>fax:   (773) 702-6648
>
>
>
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] Core.AlgorithmParam: Another column size problem

[<ju...@cs...>]

While recently working with one of our locally written plugins
which takes a SQL statement as an argument, this plugin failed
because of of the size of the field STRING_VALUE in the
Core.AlgorithmParam table:

   SQL> describe Core.AlgorithmParam;
    Name                                      Null?    Type
    ----------------------------------------- -------- ----------------------------
    ALGORITHM_PARAM_ID                        NOT NULL NUMBER(10)
    ALGORITHM_PARAM_KEY_ID                    NOT NULL NUMBER(5)
    STRING_VALUE                                       VARCHAR2(1000)
   [...]

The SQL statement I tried to run through the plugin exceeded
1000 characters.  I would think that SQL arguments would be
common for GUS plugins, and we use such plugins often at the
Preuss Lab.  A solution to this immediate problem would be to
increase the STRING_VALUE column to VARCHAR2(2000), though
eventually I or someone else may exceed this limit as well.

Just letting people know problems we are running into.

Thanks, Josef


Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [Gusdev-gusdev] ReviewStatus issues

[<ju...@cs...>]

Steve Fischer <sfi...@pc...> writes:
=>
=> [...]
=>
=> yes, that attribute will be in 3.5.
=> patching it is kind of a pain.
=>
=> i'm wondering if your use case might be better satisfied by using
=> prediction algorithm or the external_database_release_id to track who
=> made the feature.

prediction_algorithm_id, like review_status_id, does not exist
in schema version 3.0.

As for external_database_release_id  I suppose that could be
used.  So far, we have only used the External_Database/External_Database_Release
tables to identify collections of sequences.  Would this
not be against the conception of the schema to use these tables
to identify collections of features?

=> (conceptually review status has to do with what the
=> curators have done to the feature).

If one considers that the first step of the curator is to
identify a feature, then perhaps there is no conflict
between your conceptual use of SRes.ReviewStatus
and the use I have suggested?  One of the suggested
values for SRes.ReviewStatus.name, "annotated",
seems to cover this.

=> if you still want to patch it, let me know and we'll describe how.

If you could, that would be great.  There is probably no need to
send this to the list, unless others mention that they are
interested.

Thanks again!

Josef

=>
=> >My previous mail:
=> >=>
=> >=>  From: Josef Jurek <ju...@cs...>
=> >=>  To: gus...@li...
=> >=>  Message-Id: <200...@ga...>
=> >=>  Subject: [Gusdev-gusdev] Another necessary field
=> >=>  Date: Tue,  1 Feb 2005 17:35:11 -0600 (CST)
=> >=>
=> >=>
=> >=>  According to the schema browser, DoTS.NAFeature has
=> >=>  the field review_status_id which of course
=> >=>  points to a row in the table SRes.ReviewStatus.
=> >=>  However, in my installation of GUS, schema version 3.0,
=> >=>  DoTS.NAFeature lacks this field.
=> >=>
=> >=>  Such a thing would be very useful to have to distinguish
=> >=>  between the annotation of the same sequence by
=> >=>  different organizations.
=> >=>
=> >=>  In fact, I could use this field right now.  Does
=> >=>  schema version 3.2 have this field?  If so,
=> >=>  can someone suggest a patch/rebuild method
=> >=>  so that I could at least upgrade the NAFeature
=> >=>  table in my installation?
=> >=>
=> >=>  Thanks, Josef
=> >=>
=> >
=> >
=> >





Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Steve F. <sfi...@pc...>]

ed-

i'm with ya on this!  i've been trying to sort that out over the past 
couple of days.

In general, plugins must ask their users for mappings when there is an 
issue like this. 

We are moving towards SO and away from the SequenceTypes table.

The most general solution is for plugins to take a  CV mapping file.   
In this case, the plugin should have an argument --seqTypeMapFile.  The 
file is a simple tab format:

Genomic DNA    SO:0000340
DNA            SO:0000340

If we really need to handle strandness, then we need a third column in 
the middle.    We are assuming (Aaron) that any combination of sequence 
type (and strandedness) will resolve into one SO term.

If the plugin is failure tolerant (ie, tracks the work it has done) then 
we simply reject records with inputTypes not mentioned in the file.  The 
user augments the mapping file accordingly and re-runs.  Otherwise, the 
plugin should scan the input and validate against the mapping file 
before it begins to run for real.

Also, since we are moving to the SO for sequence type, we should 
probably introduce values into the SequenceType table (for our project) 
that are SO ids, like SO:0000340 (for chromosomal) rather than "genomic" 
or whatever.   Then, when we lose the SequenceType table, we'll know how 
to migrate.

steve

Ed Robinson wrote:

>On a more prosaic level, matching the sequence type is a big issue for the LoadAnnotatedSeqs plugin we are writing.  Basically, the Plugin has to do a check on the molecule type declared by the input file and match it to an entry in in the dots.SequenceType table.  The problem is that nobody is consistent with how they name their sequence types in TIGR, EMBL or Genbank.  I've handled this by allowing the plugin to throw an error if it can't find the sequence type in GUS.  Then, I enter a new entry as a subtype of a more basic sequence (Genomic DNA, = DNA, unknown strandedness).  Of course, over time, this means you end up with a ton of different entries describing the same thing.
>
>So, not only do we need to settle what our VCs are, but how we programatically handle what is not in them.  This is even worse for review status.  A lot of older plugins make assumptions about what is in the database and how it relates to their data source.  LoadGeneFeaturesFromXML is a good example.  It assumes values of 0 and 1 for specific annotation values used in the TigrXML).  
>
>Any suggestions on standard business rules for how plugins match external data to internal VCs?
>
>-ed
>
>  
>
>>From: "Aaron J. Mackey" <am...@pc...>
>>Date: 2005/02/03 Thu AM 08:40:59 EST
>>To: Steve Fischer <sfi...@pc...>
>>CC: gusdev-gusdev <gus...@li...>, 
>>	Chris Stoeckert <sto...@pc...>
>>Subject: Re: [Gusdev-gusdev] Sequence Type controlled vocab
>>
>>First, I would encourage you to look at SOFA, the subset of SO useful 
>>for sequence annotation (which is presumably what you're doing, right?)
>>
>>I would argue that these extra "attributes" you don't find explictly 
>>listed in SO are actually redundant to specific datatypes found in SO, 
>>i.e. these are encapsulated in the definition of each term.
>>
>>On Feb 3, 2005, at 7:54 AM, Steve Fischer wrote:
>>
>>    
>>
>>>Polymer Type   - no
>>> - DNA  - no
>>> - RNA - no
>>>      
>>>
>>an mRNA is RNA, not DNA; a chromosome is DNA, not RNA (unless its a 
>>viral genome, etc).
>>
>>    
>>
>>>Strandedness - no
>>>- single  - no
>>>- double  - no
>>>      
>>>
>>ditto; strandness is inherent to the definition of a type
>>
>>    
>>
>>>Sequencing process   - derived_from
>>>- Genomic - no
>>>- EST  -  SO:0000345
>>>- predicted - no
>>>- transcribed - no
>>>- what else?
>>>      
>>>
>>all of these are there, you just have to look for them in more 
>>biologically meaningful terms than what you have here.  and 
>>"derived_from" is not a SO term, it's a relationship type.
>>
>>    
>>
>>>Source - no
>>>- nucleus  - no
>>>- mitochondria - no
>>>- plastid  - no
>>>- plasmid  - no
>>>- episome  - no
>>>      
>>>
>>ditto.
>>
>>SO is/was designed to recapitulate biology (as best as possible), not 
>>the awkward attribute simplifications you seem to want to use (for 
>>instance, it seems in your scheme that I could have a sequence type 
>>that was DNA, mRNA, double stranded, predicted and episomal all at 
>>once).  With SO, you find the specific name for the thing you have ...
>>
>>To put it in a more generic context: with SO you have "integer", 
>>"unsigned integer", "long integer", "unsigned long integer", "signed 
>>integer", etc., related in a hierarchy of isa/derived_from/part_of 
>>relationships; you don't have "signed" and "unsigned", "long" and 
>>"short", etc. as singular terms.  Now if you wanted to overlay a second 
>>ontology of term relationships (e.g. the "signedness" ontology), you 
>>could relate terms by these "attributes", and have the best of both 
>>worlds.
>>
>>-Aaron
>>
>>--
>>Aaron J. Mackey, Ph.D.
>>Dept. of Biology, Goddard 212
>>University of Pennsylvania       email:  am...@pc...
>>415 S. University Avenue         office: 215-898-1205
>>Philadelphia, PA  19104-6017     fax:    215-746-6697
>>
>>
>>
>>-------------------------------------------------------
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>>by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
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>>_______________________________________________
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>>    
>>
>
>Ed Robinson
>255 Deerfield Rd
>Bogart, GA 30622
>(706)425-9181
>
>
>Sweet Caroline
>good times never seemed so good.
>I've been inclined
>to believe they never would.
>     --Neil Diamond
>
>
>We're just a bunch of idiots.
>      --Johnny Damon
>  
>

Re: [Gusdev-gusdev] ReviewStatus issues

[Steve F. <sfi...@pc...>]

josef-

a few things.

yes, that attribute will be in 3.5.

patching it is kind of a pain.

i'm wondering if your use case might be better satisfied by using 
prediction algorithm or the external_database_release_id to track who 
made the feature.  (conceptually review status has to do with what the 
curators have done to the feature).

if you still want to patch it, let me know and we'll describe how.

steve

Josef Jurek wrote:

>Steve Fischer <sfi...@pc...> writes:
>  
>
>>I am discovering other controlled vocab issues.
>>
>>First, ReviewStatus.
>>    
>>
>
>Speaking of ReviewStatus, I wrote concerning this
>field and the DoTS.NAFeature table a few days ago.
>
>Will this field be present in the NAFeature table
>in version 3.5?  Is it there now in version 3.2?
>
>
>  
>
>>The upshot is that i don't think the GUS install should provide values
>>for ReviewStatus.   It should be optional and site specific.
>>    
>>
>
>I completely agree. See below.
>
>Thanks, Josef
>
>
>My previous mail:
>=>
>=>  From: Josef Jurek <ju...@cs...>
>=>  To: gus...@li...
>=>  Message-Id: <200...@ga...>
>=>  Subject: [Gusdev-gusdev] Another necessary field
>=>  Date: Tue,  1 Feb 2005 17:35:11 -0600 (CST)
>=>
>=>
>=>  According to the schema browser, DoTS.NAFeature has
>=>  the field review_status_id which of course
>=>  points to a row in the table SRes.ReviewStatus.
>=>  However, in my installation of GUS, schema version 3.0,
>=>  DoTS.NAFeature lacks this field.
>=>
>=>  Such a thing would be very useful to have to distinguish
>=>  between the annotation of the same sequence by
>=>  different organizations.
>=>
>=>  In fact, I could use this field right now.  Does
>=>  schema version 3.2 have this field?  If so,
>=>  can someone suggest a patch/rebuild method
>=>  so that I could at least upgrade the NAFeature
>=>  table in my installation?
>=>
>=>  Thanks, Josef
>=>
>
>
>
>
>Josef Jurek, Ph.D.
>
>Daphne Preuss Laboratory
>Molecular Genetics and Cell Biology
>The University of Chicago
>ju...@cs...
>
>voice: (773) 834-3985
>fax:   (773) 702-6648
>
>  
>

Re: Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Ed R. <ed_...@be...>]

On a more prosaic level, matching the sequence type is a big issue for the LoadAnnotatedSeqs plugin we are writing.  Basically, the Plugin has to do a check on the molecule type declared by the input file and match it to an entry in in the dots.SequenceType table.  The problem is that nobody is consistent with how they name their sequence types in TIGR, EMBL or Genbank.  I've handled this by allowing the plugin to throw an error if it can't find the sequence type in GUS.  Then, I enter a new entry as a subtype of a more basic sequence (Genomic DNA, = DNA, unknown strandedness).  Of course, over time, this means you end up with a ton of different entries describing the same thing.

So, not only do we need to settle what our VCs are, but how we programatically handle what is not in them.  This is even worse for review status.  A lot of older plugins make assumptions about what is in the database and how it relates to their data source.  LoadGeneFeaturesFromXML is a good example.  It assumes values of 0 and 1 for specific annotation values used in the TigrXML).  

Any suggestions on standard business rules for how plugins match external data to internal VCs?

-ed

> 
> From: "Aaron J. Mackey" <am...@pc...>
> Date: 2005/02/03 Thu AM 08:40:59 EST
> To: Steve Fischer <sfi...@pc...>
> CC: gusdev-gusdev <gus...@li...>, 
> 	Chris Stoeckert <sto...@pc...>
> Subject: Re: [Gusdev-gusdev] Sequence Type controlled vocab
> 
> First, I would encourage you to look at SOFA, the subset of SO useful 
> for sequence annotation (which is presumably what you're doing, right?)
> 
> I would argue that these extra "attributes" you don't find explictly 
> listed in SO are actually redundant to specific datatypes found in SO, 
> i.e. these are encapsulated in the definition of each term.
> 
> On Feb 3, 2005, at 7:54 AM, Steve Fischer wrote:
> 
> > Polymer Type   - no
> >  - DNA  - no
> >  - RNA - no
> 
> an mRNA is RNA, not DNA; a chromosome is DNA, not RNA (unless its a 
> viral genome, etc).
> 
> > Strandedness - no
> > - single  - no
> > - double  - no
> 
> ditto; strandness is inherent to the definition of a type
> 
> > Sequencing process   - derived_from
> > - Genomic - no
> > - EST  -  SO:0000345
> > - predicted - no
> > - transcribed - no
> > - what else?
> 
> all of these are there, you just have to look for them in more 
> biologically meaningful terms than what you have here.  and 
> "derived_from" is not a SO term, it's a relationship type.
> 
> > Source - no
> > - nucleus  - no
> > - mitochondria - no
> > - plastid  - no
> > - plasmid  - no
> > - episome  - no
> 
> ditto.
> 
> SO is/was designed to recapitulate biology (as best as possible), not 
> the awkward attribute simplifications you seem to want to use (for 
> instance, it seems in your scheme that I could have a sequence type 
> that was DNA, mRNA, double stranded, predicted and episomal all at 
> once).  With SO, you find the specific name for the thing you have ...
> 
> To put it in a more generic context: with SO you have "integer", 
> "unsigned integer", "long integer", "unsigned long integer", "signed 
> integer", etc., related in a hierarchy of isa/derived_from/part_of 
> relationships; you don't have "signed" and "unsigned", "long" and 
> "short", etc. as singular terms.  Now if you wanted to overlay a second 
> ontology of term relationships (e.g. the "signedness" ontology), you 
> could relate terms by these "attributes", and have the best of both 
> worlds.
> 
> -Aaron
> 
> --
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  am...@pc...
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

Ed Robinson
255 Deerfield Rd
Bogart, GA 30622
(706)425-9181


Sweet Caroline
good times never seemed so good.
I've been inclined
to believe they never would.
     --Neil Diamond


We're just a bunch of idiots.
      --Johnny Damon

Re: [Gusdev-gusdev] ReviewStatus issues

[<ju...@cs...>]

Steve Fischer <sfi...@pc...> writes:
>
> I am discovering other controlled vocab issues.
>
> First, ReviewStatus.

Speaking of ReviewStatus, I wrote concerning this
field and the DoTS.NAFeature table a few days ago.

Will this field be present in the NAFeature table
in version 3.5?  Is it there now in version 3.2?


> The upshot is that i don't think the GUS install should provide values
> for ReviewStatus.   It should be optional and site specific.

I completely agree. See below.

Thanks, Josef


My previous mail:
=>
=>  From: Josef Jurek <ju...@cs...>
=>  To: gus...@li...
=>  Message-Id: <200...@ga...>
=>  Subject: [Gusdev-gusdev] Another necessary field
=>  Date: Tue,  1 Feb 2005 17:35:11 -0600 (CST)
=>
=>
=>  According to the schema browser, DoTS.NAFeature has
=>  the field review_status_id which of course
=>  points to a row in the table SRes.ReviewStatus.
=>  However, in my installation of GUS, schema version 3.0,
=>  DoTS.NAFeature lacks this field.
=>
=>  Such a thing would be very useful to have to distinguish
=>  between the annotation of the same sequence by
=>  different organizations.
=>
=>  In fact, I could use this field right now.  Does
=>  schema version 3.2 have this field?  If so,
=>  can someone suggest a patch/rebuild method
=>  so that I could at least upgrade the NAFeature
=>  table in my installation?
=>
=>  Thanks, Josef
=>




Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

[Gusdev-gusdev] ReviewStatus issues

[Steve F. <sfi...@pc...>]

Folks-

I am discovering other controlled vocab issues.

First, ReviewStatus.

On the wiki, there is a set of values for this:
  annotated
  not reviewed
  unknown

At CBIL, we have:
reviewed, correct
unreviewed
reviewed, incorrect
updated
needs re-review

What's worse, many tables required a non-null ReviewStatus, and many 
plugins use hard-coded review_status_ids in the code.

Often, the logic of a plugin is "update this row with the newly-computed 
data, unless the row has been reviewed (review_status_id == 1), in which 
case, assume it is correct, and leave it alone."  

My feeling is that ReviewStatus should be optional.

So, i think that it should always be nullable.

I also think that different sites will want to define this differently.

So, I would say that:
  1. plugins that test review status to decide whether to update the 
data or not should take on their command line a list of review status 
terms that indicate "don't update."    The plugin should query the db to 
find the review_status_ids for those (failing if not found).  If none 
are supplied to the plugin, then the plugin should not bother checking 
review status.

 2. plugins that write review status info should take a mapping from the 
values found in the input to review status  terms.  They should check 
that the review status terms are in the db, failing if not.  then, they 
can map the input to the proper review status id, and write the data to 
the db.

The upshot is that i don't think the GUS install should provide values 
for ReviewStatus.   It should be optional and site specific.

steve

[Gusdev-gusdev] GO bootstrap data

[Steve F. <sfi...@pc...>]

folks-

another proposal to simplify the provided bootstrap data.

I think the LoadGeneOntology plugin should itself load the 
GORelationshipType table, rather than requiring that as bootstrap data.

Steve

[Gusdev-gusdev] Re: why do we need GeneInstanceCategory and friends?

[Steve F. <sfi...@pc...>]

ok, i've had a better look at the Wiki in which the bootstrap data is 
described
http://www.gusdb.org/wiki/index.php/Bootstrap%20data%20II

It seems to me that the design outlined there is project/application 
specific.

I also looked at the schema, and saw that gene_instance_category_id is 
not nullable.

to me that explains why we are attempting to include the categories as 
bootstrap data.

Instead, i think it makes sense:
  - to make that field nullable
  - for any plugin that wants to fill that stuff in to enforce itself 
the values it expects there

Comments?

steve

Steve Fischer wrote:

> folks-
>
> mike and i are moving ahead putting together the new GUS 3.5 install 
> procedure.  It will include pipelines to introduce bootstrap data.
>
> Some of the data that GUS seems to need are values for:
>  DoTS.GeneInstanceCategory
>  DoTS.RNAInstanceCategory
>  DoTS.ProteinInstanceCatetory
>
> I am wondering why we need these categories.  It seems to me that if 
> the category would be implicit in the feature and/or sequence that the 
> instance is linking to.
>
> here are the suspicious values we have in CBIL's GUS for these tables:
>
> SQL> select name from Dots.RNAINSTANCEcategory;
> unknown
> mRNA
> assembly
>
> SQL> select name from Dots.proteininstancecategory;
> inferred from Assembly
> GenBank transcript
>
> SQL> select name from Dots.geneinstancecategory;
> gDG
> unknown
>
>

[Gusdev-gusdev] why do we need GeneInstanceCategory and friends?

[Steve F. <sfi...@pc...>]

 folks-

mike and i are moving ahead putting together the new GUS 3.5 install 
procedure.  It will include pipelines to introduce bootstrap data.

Some of the data that GUS seems to need are values for:
  DoTS.GeneInstanceCategory
  DoTS.RNAInstanceCategory
  DoTS.ProteinInstanceCatetory

I am wondering why we need these categories.  It seems to me that if the 
category would be implicit in the feature and/or sequence that the 
instance is linking to.

here are the suspicious values we have in CBIL's GUS for these tables:

SQL> select name from Dots.RNAINSTANCEcategory;
unknown
mRNA
assembly
 
SQL> select name from Dots.proteininstancecategory;
inferred from Assembly
GenBank transcript
 
SQL> select name from Dots.geneinstancecategory;
gDG
unknown

Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Angel P. <an...@ma...>]

Aaron,

I can't agree more with your points. Please keep up the good suggestions.

I thought a while back, GUS developers had agreed to replace CBIL's 
ad-hoc sequence ontology terms and gene models (not ad-hoc, but derived 
from EpoDB?) with SO as the major ontology for defining them. Makes 
sense to just extend the use of SO within GUS for all sequence 
categorizations.

The drawback I can see is the added layer of logic that developers must 
now know. For instance the WDK queries *may* become more complex, 
sequence annotation tools must now type sequences on defined terms, 
possibly a hierarchy of them. But since we are ditching the annot tool 
project that is not a concern. WDK queries writers would need to know 
the semantics of the current attribute model anyway, so it is not a 
stratch for them to learn sematics of SO and apply them. Also that new 
knowledge will be applicable to more than just a WDK query, so that is a 
win.

Two other advantages: 1) since it is widely accepted, most annotation 
tools should eventually provide native support for SO, and 2) we would 
more easily be able to share our gene models across GUS sites and othe 
non-GUS sites.


Angel

Aaron J. Mackey wrote:

> First, I would encourage you to look at SOFA, the subset of SO useful 
> for sequence annotation (which is presumably what you're doing, right?)
>
> I would argue that these extra "attributes" you don't find explictly 
> listed in SO are actually redundant to specific datatypes found in SO, 
> i.e. these are encapsulated in the definition of each term.
>
> On Feb 3, 2005, at 7:54 AM, Steve Fischer wrote:
>
>> Polymer Type   - no
>>  - DNA  - no
>>  - RNA - no
>
>
> an mRNA is RNA, not DNA; a chromosome is DNA, not RNA (unless its a 
> viral genome, etc).
>
>> Strandedness - no
>> - single  - no
>> - double  - no
>
>
> ditto; strandness is inherent to the definition of a type
>
>> Sequencing process   - derived_from
>> - Genomic - no
>> - EST  -  SO:0000345
>> - predicted - no
>> - transcribed - no
>> - what else?
>
>
> all of these are there, you just have to look for them in more 
> biologically meaningful terms than what you have here.  and 
> "derived_from" is not a SO term, it's a relationship type.
>
>> Source - no
>> - nucleus  - no
>> - mitochondria - no
>> - plastid  - no
>> - plasmid  - no
>> - episome  - no
>
>
> ditto.
>
> SO is/was designed to recapitulate biology (as best as possible), not 
> the awkward attribute simplifications you seem to want to use (for 
> instance, it seems in your scheme that I could have a sequence type 
> that was DNA, mRNA, double stranded, predicted and episomal all at 
> once).  With SO, you find the specific name for the thing you have ...
>
> To put it in a more generic context: with SO you have "integer", 
> "unsigned integer", "long integer", "unsigned long integer", "signed 
> integer", etc., related in a hierarchy of isa/derived_from/part_of 
> relationships; you don't have "signed" and "unsigned", "long" and 
> "short", etc. as singular terms.  Now if you wanted to overlay a 
> second ontology of term relationships (e.g. the "signedness" 
> ontology), you could relate terms by these "attributes", and have the 
> best of both worlds.
>
> -Aaron
>
> -- 
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  am...@pc...
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004

Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Aaron J. M. <am...@pc...>]

First, I would encourage you to look at SOFA, the subset of SO useful 
for sequence annotation (which is presumably what you're doing, right?)

I would argue that these extra "attributes" you don't find explictly 
listed in SO are actually redundant to specific datatypes found in SO, 
i.e. these are encapsulated in the definition of each term.

On Feb 3, 2005, at 7:54 AM, Steve Fischer wrote:

> Polymer Type   - no
>  - DNA  - no
>  - RNA - no

an mRNA is RNA, not DNA; a chromosome is DNA, not RNA (unless its a 
viral genome, etc).

> Strandedness - no
> - single  - no
> - double  - no

ditto; strandness is inherent to the definition of a type

> Sequencing process   - derived_from
> - Genomic - no
> - EST  -  SO:0000345
> - predicted - no
> - transcribed - no
> - what else?

all of these are there, you just have to look for them in more 
biologically meaningful terms than what you have here.  and 
"derived_from" is not a SO term, it's a relationship type.

> Source - no
> - nucleus  - no
> - mitochondria - no
> - plastid  - no
> - plasmid  - no
> - episome  - no

ditto.

SO is/was designed to recapitulate biology (as best as possible), not 
the awkward attribute simplifications you seem to want to use (for 
instance, it seems in your scheme that I could have a sequence type 
that was DNA, mRNA, double stranded, predicted and episomal all at 
once).  With SO, you find the specific name for the thing you have ...

To put it in a more generic context: with SO you have "integer", 
"unsigned integer", "long integer", "unsigned long integer", "signed 
integer", etc., related in a hierarchy of isa/derived_from/part_of 
relationships; you don't have "signed" and "unsigned", "long" and 
"short", etc. as singular terms.  Now if you wanted to overlay a second 
ontology of term relationships (e.g. the "signedness" ontology), you 
could relate terms by these "attributes", and have the best of both 
worlds.

-Aaron

--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  am...@pc...
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697

Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Steve F. <sfi...@pc...>]

Aaron encouraged me to take a second look at SO.   (my first look came 
up dry, and i surmised that it was more "feature" oriented than 
"sequence" oriented)

the results are below

But first, here are the term in CBIL's SequenceType table:
DNA
RNA
ds-DNA
ss-DNA
ss-RNA
ds-RNA
mRNA
EST
tRNA
rRNA
unknown
predicted_mRNA
virtual
GSS
oligonucleotide

To, me, this is confuting multiple concepts: polymer type, strandedness, 
molecule

But, I am now thinking that if we replaced that list with the following 
attributes and values, we would probably be just fine.  SequenceType 
here *is* confuting multiple concepts, but, in a way that i think will 
satisfy intuition and reasonable querying needs:

  Singlestranded 
     true
     false
  SequenceType:
     chromosomal
     mRNA
     rRNA
     tRNA
     EST
     oligo
   HasPieces   (is virtual)
      true
      false   

Now for the SO survey:

Polymer Type   - no
  - DNA  - no
  - RNA - no

Molecule - no
 - chromosome  - SO:0000340
  - mRNA -  SO:0000234
  - tRNA -  SO:0000253
 - rRNA -  SO:0000252
 - oligo -  SO:0000696
Strandedness - no
 - single  - no
 - double  - no
Sequencing process   - derived_from
 - Genomic - no
 - EST  -  SO:0000345
 - predicted - no
 - transcribed - no
 - what else?
Source - no
 - nucleus  - no
 - mitochondria - no
 - plastid  - no
 - plasmid  - no
 - episome  - no

Guess what, all the sequence types in my proposed list above are found 
in the SO:
 - chromosome  - SO:0000340
  - mRNA -  SO:0000234
  - tRNA -  SO:0000253
 - rRNA -  SO:0000252
 - oligo -  SO:0000696
  - EST  -  SO:0000345

But, does that mean we should abolish the SequenceType table?    If we 
do, then a sequence would point to the SO for its type.   The advantage 
is that we will be out of the business of inventing yet another CV.   
The disadvantage is that now users have to wade through 400+ terms to 
find the 6 that we think are relevant

????

steve


Steve Fischer wrote:

> folks-
>
> Having looked at SO and MGED, I am not sure they are capturing what I 
> have in mind, or, what we have captured in our SequenceType table
>
> Here is the way I am thinking about breaking down "sequence type."   
> (If somebody can show me how these map into either of the ontologies 
> Chris has mentioned that would be great).
>
> For NA sequences:
>
> Polymer Type
>  - DNA
>  - RNA
> Molecule
>  - chromosome
>  - mRNA
>  - tRNA
>  - rRNA
>  - oligo
> Strandedness
>  - single
>  - double
> Sequencing process
>  - Genomic
>  - EST
>  - predicted
>  - transcribed
>  - what else?
> Source
>  - nucleus
>  - mitochondria
>  - plastid
>  - plasmid
>  - episome
>
> Steve
>
> Chris Stoeckert wrote:
>
>> Steve,
>> There are two complementary standards for sequence type. One comes 
>> from the MGED Ontology.
>> see 
>> http://mged.sourceforge.net/ontologies/MGEDontology.php#BioSequenceType
>> The other is SO  http://song.sourceforge.net/
>> Chris
>>
>> On Feb 2, 2005, at 5:14 PM, Steve Fischer wrote:
>>
>>> folks-
>>>
>>> in gus we have a Dots.SequenceType table.
>>>
>>> here are the columns:
>>> nucleotide_type
>>> sub_type
>>> strand
>>> hierarchy    [should be hierarchy_depth]
>>> parent_sequence_type_id
>>> name
>>> description
>>>
>>> First question:  does anybody know of an "emerging standard" for this?
>>>
>>> If there is one, then we should include it in the Controlled Vocabs 
>>> that we package with GUS.
>>>
>>> Otherwise, we have, I think, two candidate SequenceTypeCVs:
>>>   - the one provided by Sanger on the wiki:  
>>> http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
>>>   - the one currently housed in CBIL's GUS instance
>>>
>>> As part of the GUS 3.5 install, we are getting serious about making 
>>> the loading of CVs much easier.   A central part of that is making 
>>> the CVs available from CBIL's download site (eg, the CBIL anatomy CV).
>>>
>>> So, i am thinking that CBIL should chose one (or more) sequence type 
>>> CVs to provide as downloads.  They could be offered in GUS XML format.
>>>
>>> Then, the automated GUS CV installer would find them from CBIL just 
>>> like it will find GO from the GO Consortium.
>>>
>>> Any plugin that uses SequenceTypes should *not* hard code the 
>>> transform, but, instead, take a SequenceTypeMapping file.  The file 
>>> specifies the mapping from input sequence type to that stored in gus 
>>> (by name).  The plugin should pre-scan the input file to detect if 
>>> there are any illegal sequence types, and warn the user before 
>>> loading any data
>>>
>>> If users find sequence types that the CBIL CV is missing, they can 
>>> propose them via the mailing list.
>>>
>>> The objective is to:
>>> 1. work with the fact that different input files for a plugin may 
>>> use different sequence types
>>> 2. get out of the business of ad hoc changes to the sequence types 
>>> stored in the db
>>>
>>> comments?
>>>
>>> steve
>>>
>>> as a candidate CV the Sequence the SequenceTypesCV as developed by
>>>
>>> If not, then, how about this.   Plugins that depend on sequence type 
>>> use a standard config file for sequence type.  (this might apply to 
>>> other loose CVs).  The config file specifies the
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
>>> Tool for open source databases. Create drag-&-drop reports. Save time
>>> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
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>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>>
>>
>>
>> -------------------------------------------------------
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